It's Time to Begin
by Follow-ur-Shadow
Summary: Elizabeth unascends and returns to Atlantis but things have changed, including the relationships she left behind. Sparky.
1. Chapter 1

It's Time to Begin

 **Category** : Angst/Hurt Comfort/Romance

 **Pairing** : Sparky

 **Summary** : Elizabeth unascends and returns to Atlantis but things have changed, including the relationships she left behind.

 **Warnings** : None.

 **Disclaimer** : Own nothing.

 **Authors Notes** : I've been reading the Stargate Atlantis Legacy series and it inspired me to write my take on Elizabeth unascending. Hope you enjoy! :)

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John's pulse thudded loudly between his ears drowning out Carson's thick Scottish accent, the words blurring around him. The weight of the doctor's findings crashed down and his chest tightened in anticipation. Elizabeth was alive. That was all he cared about, all he needed to know.

Teyla's touch feathered against his arm reminding him to breathe and he shifted ever so slightly to keep his balance. He didn't care about the explanation, the science behind unascension or how it had transpired. The women Lorne's team had found off-world was _his_ Elizabeth.

Breaking free from the group he ignored Carson's warning as he pushed through the doors to the infirmary.

She was perched on the edge of the bed and he met her gaze his stride faltering as the air left his lungs like a vacuum. She was exactly as Woolsey had described, every inch of her original form right down to the ghostly smile that played on her lips and he took a step forward fighting the sudden sting behind his eyes.

" _Hey_..."

Elizabeth was drawn to his presence. Even though her memory was still hazy, coming back in bits and pieces, his appearance felt natural and she eased herself from the bed moving towards him.

"Hey yourself."

She stopped in front of him pausing for a beat. Even though he looked uncertain she couldn't fight her instincts and her arms snaked around his neck feeling a familiar sense of Déjà vu as she gripped him tightly.

He squeezed her in response ignoring the doubt that screamed her return wasn't possible. He was terrified it wasn't real, that he'd lose her again but after so many failed second chances he was equally afraid of letting her go. He needed hope, anything to lure him away from the darkness that had started creeping in and he ignored the sudden guilt clawing his throat. He'd left her behnd but the apology brimming on his lips wasn't enough to make it right. Words couldn't undo the three years she'd been gone but she was home now, safe in Atlantis.

No matter what it took he'd make damn sure it stayed like that.


	2. Chapter 2

John fidgeted awkwardly, eyeing Woolsey from across the desk before glancing around what used to be Elizabeth's office. So much had changed in the last three months but some things had an eerily familiar, almost surreal feeling to them.

Elizabeth had been allowed to stay in Atlantis as a correspondent but she was no longer in command reporting to Woolsey who monitored her progress. She'd been working with a psychiatrist to recover her memories and the IOA were in agreement, as long as she passed the necessary evaluations she would still be deemed an asset to their mission.

Of course she'd passed with flying colours but his relief had been overshadowed by the reality of what that meant going forward.

"You're asking me if I think she's ready?" He threw the question back at Woolsey who simply nodded his head in response.

It was no secret the two of them had been spending a lot of time together since her return. They'd been close before so it was only natural they'd gravitated towards each other again and John assumed the man was asking out of courtesy. He'd heard about the mission, brokering relations with a race called the Hindorians who were known to be reserved in their dealings with other cultures. They were an advanced democratic civilization and the IOA were pushing to get them on aside apparently with the newly formed idea that Elizabeth would head the talks.

The catch, the decision to allow her off-world to lead the negotiations.

"She's been cleared and the IOA want this to happen," Richard pushed the briefing folder across the table, "I'm asking what _you_ think."

John picked up the papers more for show than anything else. Truthfully he didn't give a damn about what the file contained he didn't want her out there, end of story. The idea that she'd be at risk so soon after returning made him feel uncomfortable and he dropped the folder back on the desk swallowing roughly.

"I think it's too soon."

Richard considered the statement knowing his superiors wouldn't like it but still willing to listen to both sides. It was his call but he wanted to be absolutely sure before he made the decision. "May I ask what you're basing that on?"

"All I'm saying is, it wouldn't hurt to give her a little more time to adjust." John shifted uncomfortably, finding the words difficult to part with. He knew she was strong and didn't doubt her abilities but anyone would be struggling with the trauma she'd been through, much less be able to compartmentalize it all in a few months.

"I see." Richard regarded the man trying to discern if his suggestion held any merit or if he was simply being over protective. Losing Doctor Weir had hit Atlantis hard and to have her returned was indeed a miracle. No one would blame him for wanting to be cautious. "Thank you Colonel, I'll take that under advisement."

John nodded sharply as he pushed up from his seat. Elizabeth wasn't going to like it when she got wind of his recommendation but if it meant keeping her safe he was willing to wear the brunt of her anger. He'd sworn to himself he'd go to any lengths to protect her and he'd meant it.

There was no way in hell he was losing her again.


	3. Chapter 3

John watched the waves crashing below him, the wind catching his hair as he gazed down at the ocean. He'd been hoping for a few minutes of peace and quiet but the door whooshed open and he winced, tightening his grip as Elizabeth's voice carried across the short distance.

"We need to talk."

Her tone was tight and a sigh pulled from his lips as she moved to join him. He'd been expecting the conversation. He'd just hoped for a little more time to get his thoughts in line first. "Look, I know what you're going to say..."

"You went behind my back-" she cut him off, a stab of hurt betraying the anger beneath her words, "you undermined me in front of Woolsey and now he's reconsidering the mission. I highly doubt you can imagine the colourful language I'd like to use right now."

His grip on rail loosened and he titled his head towards her. She was pissed -he got it- but her firm expression didn't sway his resolve. "He asked for my opinion, I gave it. I'm sorry if it wasn't what you wanted to hear."

The statement was blunt and she steeled herself against his disapproval. After everything she'd been through she'd have thought, out of everyone, he would've been the one to back her up. Clearly she'd been wrong but if he didn't like it _fine._ He was right, it was just an opinion. "I appreciate that... which is why if the mission gets cleared I'm going to request Major Lorne's team as backup."

Frustration shattered his calm facade and he turned, annoyance drawing his brows together. This wasn't a negotiation. If Woolsey agreed to let her off-world she was going with him or not at all. He'd make damn sure of it. "Like hell you are."

She didn't flinch at the show of stubbornness, if anything it only fueled her determination. "If we're out there and you don't trust I can do my job, you're the liability not me-" she crossed her arms, squaring her shoulders, "and I'm certain my opinion counts for something as well."

He stared her down, a deep growl building in his throat. His recommendation had nothing to do with trusting her ability. She was bargaining with him right now, admittedly doing a bloody good job of it, but that wasn't going to keep her safe out in the field. "You've only been back a couple of months," his voice was rigid and he swallowed trying to make her understand. He wanted to protect her. Placing her directly in the line of fire so soon after her return was reckless and he was prepared to stand his ground on the matter. "I'm not doubting you, I just think a little more time to adjust wouldn't hurt."

She saw a flash of concern in his gaze and her chest tightened in response. She knew he was worried but it wasn't his decision, it was something she needed to do for herself and a strained sigh worked its way from her lips, "I can see why you're hesitant but it's not your call, I'm ready-"

"I'm not!"

The outburst made her flinch and she frowned as he turned away, his hands catching the rail with a death grip. The show of emotion was rare, unlike him, but she didn't shy away suddenly realizing she'd misread the situation; he wasn't just concerned, he was doubting _himself._

"We haven't really talked about..." she stopped, the words overtaken by a tense pause. She'd ordered him to leave her behind. They'd both been acting in Atlantis' best interests but that didn't make the discussion an easy one. It was complicated but no matter how hard it was to navigate, she didn't blame him. "What happened to me wasn't your fault..."

The reassurance felt hollow and he stiffened as she stepped closer to him. Her fingers brushed his and it took all his willpower not to give into his guilt and tear away. He knew what she was doing but forgiveness wasn't going to change anything. "I let you go-" he admitted, the truth barely above whisper, "doesn't matter why, I still lost you."

"I know..." she agreed, understanding what he'd been through. He'd always worn the deaths of his men as failures and she couldn't change that. All she could do was remind him that they'd all had a choice and it had been her decision to remain behind. "We lose people John and it's never easy but everyone here in Atlantis knows the risks. It's what we signed up for."

"You don't get it." He breathed in sharply, trying to draw the strength the make her understand. He wasn't good at this -the whole talking thing- and before the words even left his mouth they were buried beneath a wave of frustration, "I didn't sign up for _this-_ " he motioned between them with an errant hand,"I didn't come here to fall... to care about someone. I came here to do a job that's it."

It was too late to take it back and he watched her eyes widen in response. There was no point denying it now. His feelings had blind-sided him but they were there, had been for a long time, and he'd been living with the consequences ever since he'd lost her.

She opened her mouth trying to ascertain exactly what he meant but for once she didn't trust her instincts to read him properly. They'd always been close, she'd always cared about him but had she been naive to believe those feelings were based on friendship? Or was she simply reading too much into it now?

Her hesitation was obvious and embarrassment flushed his features.

She didn't feel the same way, messaged received loud and clear... but that wasn't her problem, it was his. Maybe he was the one who had an issue compartmentalizing. "You should go on the mission-" he conceded, his emotions too unsteady to continue pushing his argument. He didn't know what to do anymore, what he could trust and he backed away catching her gaze briefly, "I'll speak to Woolsey and you're right, I think Lorne's team can handle it."

" _John_..."

She called out for him to stop but he didn't break stride exiting the balcony without any further acknowledgment. She wanted to chase after him, demand to know what he'd meant but she knew the attempt would probably be futile.

They both needed time, something she'd come to learn was essential in order to move forward.


	4. Chapter 4

Elizabeth let her gaze wash over the control room, the inactive gate sitting at the center of her thoughts. Woolsey had given her mission the green light and she'd spent most of the night prepping but she'd found her focus wandering at times, lingering on John and the argument they'd had. She'd wanted to talk to him before departing but he'd been avoiding her and Lorne's team would be ready and geared up in less than an hour.

A sigh pulled from her lips, the conversation would just have to wait until she got back.

" _Elizabeth?_ "

Jennifer waved her her hand, surprised that the Doctor hadn't answered the first time she'd called. Even as she came to a standstill beside her friend it took the women a few seconds to snap out of her thoughts and she lent over the control console, keeping her tone light as she voiced her concern, "everything okay?"

Elizabeth drew her arms over his chest forcing a smile. "Yeah, sorry... I was just thinking."

"About the mission?" Keller guessed, having already heard the rumors through Rodney. Usually she didn't like to entertain his gossiping but she'd signed off on the paperwork deeming Elizabeth fit for active duty. If she was having second thoughts then it was her responsibility to address them. "I know it must be daunting."

"It's not that-" she jumped in quickly then paused taking a moment to align her thoughts. There was no point lying. Anyone in her position _should_ be feeling somewhat nervous and there was no shame in admitting her reservations."It's not _just_ that," she corrected stealing a breath "I know what's at stake but I'm ready. I need... I _want_ to do this."

Jennifer nodded, believing the statement to be true. They'd been working closely over the last few months and she'd learn to pick up on when the diplomat was avoiding the truth but she also knew when the women was deflecting. "This wouldn't have anything to do with Colonel Sheppard would it?"

Elizabeth stiffened though she shouldn't have been surprised. World traveled fast around Atlantis, clearly something that had remained the same in her absence. "I'm assuming you heard about his recommendation?"

Answering a question with a question. Jennifer knew it was a tactical move but if anything it proved her friend was definitely ready for the scheduled mission, just not to discuss what was really bothering her. "You were cleared weeks ago, I'm sure he was just being overly cautious."

Elizabeth drew her lips together releasing a hum of uncertainty. Every time she thought back to their confrontation the truth slipped further from her grasp. Had he really been alluding to the feelings between them or had she simply imagined it? Did part of her merely want to wish it was true?

"Can I ask you something?" She swallowed the question, clasping her hands awkwardly behind her back. The aftermath of her death wasn't an easy topic to bring up in part because she wasn't sure she had a right to know about it. Was it egotistical to ask if she'd been mourned, _missed_?

"I ordered him to leave me behind, at the time I didn't think about the personal ramifications that might follow..."

A pause fell between them and Jennifer felt a wave sympathy wash over her. Even though it wasn't an actual question she suspected she knew what was coming next and why it was so difficult to ask. "He fought for months to launch a rescue mission but the logistics... it would have been a suicide mission. We all found it difficult to accept but Colonel Sheppard took it the hardest."

The truth fueled the guilt Elizabeth already felt and she shifted uncomfortably. It didn't clarify the extent of John's emotions but it helped her to understand or at least she thought it did. "So you think it's possible he was just being over protective?"

Keller bit the inside of her mouth, the smallest of smiles catching her off guard. She wasn't blind and neither was the rest of Atlantis. Since Elizabeth's unascension both she and John had been practically inseparable and if they weren't both so stubborn, maybe they'd be able to see it for themselves. "I'd say it's a little more than that."

The teasing tone cause Elizabeth to glance up, her brows drawing together at the Doctor's subtle wink. She wanted to read more into it but embarrassment clouded her judgement and she ducked her head away from the scrutiny.

She had a mission to focus on, now wasn't the time to be analyzing her relationship with John. "Thank you." It was said with genuine gratitude despite the fact they both knew it was a brush off. Even if she'd wanted to continue the conversation time wouldn't allow it and she breathed in deeply as she left Jennifer standing alone in the control room.

xx

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xx

Lorne knocked on the door to John's dimly lit office, stealing a hesitant breath as the Colonel glanced up from his laptop. He wasn't in the habit of rubbing his superiors up the wrong way but Doctor Weir was someone he regarded a friend. Back in the early days of their mission, before her disappearance, they'd spent a lot of time together awaiting the return of Atlantis' flagship team. He'd happy taken on the responsibility, filling in the Colonel's role by her side, but the moment John had reappeared it was clear who rightfully held the position.

"Something you needed Major?" John lent back in his chair, his expression cool as he regarded the man opposite him.

Evan tensed but didn't let it show as he stepped further into the room. He was a military man and he didn't back down from an awkward conversation, not unless it was likely to get him court-marshaled. "I just wanted to let you know Sir, Doctor Weir and our team are ready to depart."

"Glad to hear it." John remained impartial as he drew his gaze back to the screen in front of him. He'd been playing solitaire for the better part of an hour, trying to ignore the fact he knew _exactly_ when their mission was due to depart but so far all he'd achieved was the longest three card move in history.

Even though the comment was clearly intended as dismissal Evan stood his ground, clearing his throat when the silence became too much. John glanced up at the sound and he shifted clasping his hands behind his back, "permission to speak freely Sir?"

"Do I have a choice?" John scrubbed a hand through his hair breathing out a sigh. They'd always been loose in regards to their chain of command outside of a military situation and he had a lot of time and respect for the man but he could already sense he wasn't going to like where the conversation was going.

Evan relaxed slightly but didn't let his guard down completely. He knew it was a delicate situation and he chose to remain standing as he approached it. "I know you have reservations about sending Doctor Weir off-world but we're going to take good care of her... and if it helps, I personally won't be leaving her side."

John still didn't like the idea but despite his hesitation he felt some of the pressure ease knowing he could trust the man in front of him.

"...and I know she'd really appreciate it if you came to see us off."

And there was the catch, he thought, checking the timer on his game of solitaire.

Truthfully he'd wanted to clear the air between them days ago but he didn't know how to defend his actions without revealing exactly why he didn't want her to go. He'd come close to admitting his feelings on the balcony and he'd only just managed to escape the embarrassment of actually saying them out loud. Avoiding her had seemed like the least messy solution but part of him couldn't stand the idea of her leaving with them on bad terms.

Making the decision he closed his laptop, swallowing his pride as Lorne stepped back to allow him past.

Apparently his compliance was enough because the rest of the journey to the gateroom was made without any further comment on the situation. Silence he was grateful for until they parted ways, the Major heading down to join his team in front of the gate. With a surprisingly steady maneuver he took his position behind the control panel, catching Elizabeth's gaze as she glanced up. It was like she sensed he was there and for a brief second neither of them moved until a small smile floated on her lips urging him to press the interface system.

"Doctor Weir... try not to start any civil wars out there."

He watched her tap the side of her ear piece, her voice flooding the space around him.

"I'll try my best Colonel..."

The gate activated behind her and he breathed out slowly.

He trusted her and he trusted Lorne to keep her safe.

He just had to hope that was enough.


	5. Chapter 5

John slowed his pace trying to act casual as he knocked on the door to Elizabeth's quarters. He'd been in the gateroom for the teams arrival they'd been ushered away for the usual checks and the debriefing had taken the better part of an hour to get through. Even though he'd wanted to give her some time to catch her breath before he checked in on her, his relief at having her home out weighed his patience and he shifted nervously as she appeared in front of him.

Elizabeth smiled, the small gesture fighting the lines of exhaustion that had become a permanent fixture since she'd gated off-world. The mission had been a success but taxing and she leaned against the doorframe truly relieved to see him.

He returned her smile, their standard greeting rolling off his tongue, " _hey_..." It felt natural but there was still a slight air of tension hanging between them and he let his gaze wash over her, "you okay?"

She read the genuine concern in his expression and her lips curved in order to reassure him, "I'm fine." A yawn started to build but she held it back, fighting the need to lie down. "It's been a long couple of days-" she admitted, folding her arms over her chest, "but the Hindorians are willing to accept us as trading partners. Now it's just a matter of finalizing the negotiations."

He nodded having already heard the outline in the briefing. Honestly he hadn't come to talk about the mission but his thoughts stalled and he jabbed his hands down into his pockets as a semi-awkward silence spilled between them. Apparently he hadn't prepared for _any_ conversation. "I should probably let you get some rest..."

"John." She used a firmer tone to stop him from leaving. She was exhausted but they'd waited long enough to resolve their issues and she'd sleep a whole lot better knowing exactly where they stood. "We should talk."

"Now?" He shifted uncomfortably but her pointed look suggested there was no getting out of it. Maybe it was for the best, if she was this tired he might get a little leeway and maybe she'd conveniently forget the whole thing by the morning. Cutting his looses he gave a slight nod, clearing his throat as he followed her inside.

"So..." he started, glancing around distractedly as she sat down on the bed, "how was the weather?"

A smirk tugged her lips and she raised an eyebrow in response. "It was... unavoidable."

He nodded awkwardly. Apparently they were diving straight in and he couldn't help muttering under his breath, "I'm sensing there's a theme here."

The slight amusement she'd shown dropped from her expression, replaced with something akin to a disappointed teacher, and he sighed hoping to get the conversation over and done with as quickly as possible. "Look, about what I said-"

"Or didn't say." She quickly pointed out his allusiveness.

" _Right._ " He agreed, moving to perch beside her on the bed. Technically he hadn't 'said' anything so much as implied it but in his mind the implication was pretty damn clear. He cared about her -too much- and he'd let that impact his judgement. "I overreacted-" he steered away from the reason why, swallowing roughly, "but it won't happen again. We don't need to take it any further than that."

Again it was an offhanded dismissal and she steeled herself against his unwillingness to talk. She wanted to hear him say it out loud, in the very least acknowledge what they were talking about and she softened her voice pushing the discussion. "Did you mean it?"

"That thing that I didn't say?" He questioned, nervously twisting his hands together. He didn't know why she was purposely trying to be difficult but he couldn't take it back now and if she wouldn't accept his out, then he didn't have much of a choice.

"Yeah..." he finally admitted, dropping his gaze to the floor, "I meant it."

She was surprised by the comment and opened her mouth but promptly closed it again wanting to choose her words carefully. It took a moment but her thoughts finally settled on what she wanted to ask. "Is this a... recent thing?"

"No-" he breathed in sharply, "yes, _maybe,_ I don't know."

He scrubbed his face not sure how to answer the question. It was complicated but at the end of the day it didn't really make any difference "It doesn't matter-" frustration crept into his tone, his hand falling back down to rest on his leg, "it was inappropriate of me to bring it up. I shouldn't have said anything."

She humored him trying to ease the tension between them. "You didn't."

" _Right_." He hoped it was enough, that it would draw a natural end to the conversation and when she didn't say anything in return he took it as his cue.

"So... good talk." _Let's never do it again_ , he thought, about to push himself up when her fingers stilled on his thigh. He glanced down at her hand then back up to her timid expression trying to read her intention. He had no idea what was happening but his heart slammed in his chest as she shifted closer to him.

" _Elizabeth_?"

He was a man of action, instinct, and the warning in his tone was clear but she didn't back away. Instead she sat like a deer caught in headlights and he seized the opportunity to kiss her, his lips moving slowly against hers to test the idea. In his opinion it passed with flying colours but he forced himself to stop, edging back to search her gaze for permission. The slight curve of her smile was all the encouragement he needed and he lifted his hand to her cheek cupping her face so he could deepen the kiss.

xx

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 **AN: Thanks so much for the reviews! Just a quick note, this isn't the end... there's still a lot more drama and angst to come! Did Lorne and Elizabeth really make it back unscathed? I don't think so...**


	6. Chapter 6

John blinked trying to shake the fog clouding his brain as his body adjusted to waking up. The room was muggy, the stale air jolting his memory and a lazy smile spread over his face. He and Elizabeth had definitely worked out their issues and his muscles tingled tight with the anticipation of exploring the new development.

Rolling over he slipped his arm beneath the covers but frowned when he came into contact with her skin. It was blistering with heat and he drew back the blanket, squinting through the darkness. "Liz'beth?" He mumbled her name but she didn't respond and he waved on the light, reaching down to check her pulse. It was strong and steady but her face was flushed with sweat and he shook her shoulder trying to rouse her.

She grunted disapprovingly at the disruption wincing as light splintered her vision. It was too bright and she groggily pull away from him burying herself beneath the covers.

"You've got a fever-" he touched her shoulder again, concern knotting his brow. Living in Atlantis meant they were always on call and as far as he knew she was a light sleeper. It wasn't like her to be despondent. With a shrug he quickly rolled the other way sliding off the mattress to put his trousers on. He wasn't about to take any chances with her health -not given she'd just been offworld- and once he was dressed he rounded the bed, pulling the blanket off her. "Elizabeth come on, open your eyes for me."

She protested again but followed the instruction, flinching in confusion. Her head was pounding and when he asked her to sit up she struggled with the movement, not entirely certain if she was going to manage it without throwing up or passing out.

" _Easy..._ " he helped her perch on the edge of the mattress, "I'm taking you down to see Carson, no arguments."

She recognized the stubborn set of his tone and wasn't sure she had the energy to argue. She even obliged when he began dressing her. Once he was finished his touch lingered on her knee, giving it a gentle squeeze.

"You okay? His hand hovered as he waited for confirmation. She looked exhausted and not in the 'good-kind- of-way' he would have liked to take credit for.

"Dizzy," she admitted swallowing roughly. Her throat felt like the Sahara Desert, every one of her muscles was screaming in protest and it took most of her strength to push up from the bed. The room lurched and he caught her around the waist, his hold keeping her steady.

"I've got you."

She murmured in response and he swung his arm below her knees, lifting her up off the ground and pulling her against his chest. Something was _definitely_ wrong and his concern peaked as he carried her out of the small quarters. By the time he reached the infirmary she was out cold and he pushed into the room surprised to see McKay and Keller already there.

Jennifer spotted the pair first and rushed towards them, Rodney hot on her heels. "What happened?" She glanced over Elizabeth's unconscious form, assessing the symptoms she was unfortunately already familiar with. She and Rodney had found Lorne in a similar way and she motioned to nearest bed.

"She was running a fever, complaining of dizziness then she just collapsed." John gently placed her down, his gaze darting around the small space. "I thought Beckett was on duty tonight?"

"He is." She pulled out a penlight to check Elizabeth's pupils. "Major Lorne was in the mess when he started showing the same symptoms, Carson's running tests on him now but we need to get the entire team in here and checked."

John nodded, tapping his ear piece. "Peters?" He waited for confirmation the Major had heard him before speaking again, "I need you to find Evers and Green, get them to report to the infirmary immediately." A familiar 'yes Sir' burst through the static and he shut off the channel watching Keller move around Elizabeth. "How's Lornes doing, any idea what we're dealing with?"

"It looks like it could be viral-" Carson entered the room, reading from the tablet in his hand, "I've got the Major started on an IV line but we won't know more until his bloods come back."

"Viral, as in contagious?" Rodney pipped up, a worried expression appearing on his face, "I mean obviously I'm concerned for them-"

"Aye, just more concerned with yourself." The Doctor breathed out a sigh, referring back to the electronic data. Even though it was inconclusive he had enough to hypothesize. "It looks to be an infection of sorts, there's no reason the believe we're in any immediate danger."

John bit down hard on his lip. They might be safe in close proximity but he and Elizabeth had just taken 'close' to a whole other level that would definitely have put him at risk. "You need to test me-" he blurted it out, wincing as the group turned to look at him.

Keller placed the penlight back in her pocket, glancing up at him, "Colonel, it's unlikely this could be passed on like a common cold. Even if it was you would have had to spend a significant amount of time in close-"

"Test me." He said it again, this time more firmly as he held her gaze for a beat. He really didn't want to go into detail, especially not in front of-

" _Why_?' Rodney shot him a confused look.

"That's really not important." John locked his jaw, still keeping his eyes trained on the female doctor. Whatever she read in his expression, it seemed to be enough, because her cheeks coloured as she gave him a subtle nod.

"No, no... it kind of is-" McKay persisted, "I mean, do you feel sick? What if it _is_ contagious?"

"Rodney's right," Carson admitted, reluctantly siding with the scientist, "if there's a reason you think you might be infected-"

" _Guys._ " Jennifer cut them off, ducking her and breathing out a sigh. There was no way around it but she settled on what she hoped was an evasive but satisfactory answer. "What Doctor Weir and the Colonel choose to do in their own time is _private_."

John appreciated the tact but could already see the cogs spinning in McKay's head, the man's eyes bulging as he deciphered the cryptic piece of information.

"Oh _-_ " Rodney's mouth dropped open as he processed the meaning, "you were and _she_.. I mean, you two were..."

"You're right Colonel-" Carson jumped in, doing everything he could to mask his own surprise at the revelation. Now certainly wasn't the time or the place for gossiping. "We should get you tested to be certain, follow me."

John felt a rush of embarrassment as he left Keller taking care of Elizabeth. It wasn't how he'd wanted the truth to come out and no doubt she'd be pissed about it when she woke up but that had to happen first. They had no idea what they were dealing with and he gave her one last fleeting glance as he tailed Becket out of the room.

"When did they-"

"Not the time Rodney." Jennifer silenced him, focusing on the unconscious women. She was happy for them but as usual life in Atlantis never ran a smooth course. Now it was her job to make sure they got the second chance they deserved.


	7. Chapter 7

"Colonel, how are you feeling?"

John glanced up from the chair beside Elizabeth's bed, rubbing his eyes tiredly as Keller approached him. It had been nearly three hours since she and Lorne had been admitted and although Carson's results had come back conclusive, proving it was a viral infection, they were still no closer to finding a cure.

"Fine..." he mumbled the word rolling up his sleeve so the doctor could take more blood. They'd spotted an abnormality in his white cell count but still had to do more tests to find out if it was related or not. "How's Lorne?" He asked, wincing as she stuck the needle in.

"He responded briefly to the last round of treatment but the effects are wearing off again. Whatever this thing is it's resilient." She filled two viles and placed them in a plastic ziplock bag before checking Elizabeth's vitals. They'd been trying her on a different combination of drugs to the Major hoping one would provide an answer but as she thumbed through the information a heavy weight settled in her chest. Like Evan, there was little to no improvement.

John read her expression and dropped his head, rolling his sleeve down again. He'd noticed Elizabeth's breathing had become more shallow and was almost expecting the bad news but it didn't make it any easier to hear. "There has to be something else we can do."

"She's fighting Colonel-" Jennifer tried to reassure him, "and Rodney's in his lab working on a plan b."

He wished the fact was more comforting but their plan b consisted of trying to find something in the Atlantean database to help. It wasn't exactly a ground breaking second strike. They had more chance going back to the planet to look for answers, he just had to convince Woolsey of that. "Evers and Green?"

"Still showing no signs of the infection." She confirmed, bringing their results up on her tablet. However Lorne and Elizabeth had become infected it seemed to be an isolated event.

"So we've got no idea how this could have happened?" He asked, scrubbing a hand up through his hair. He'd been in the briefing. He knew there was a significant amount of time that the the team had been separated whist the negotiations were taking place but there had to something they remembered that could help.

"I'm sorry Colonel-" she said, feeling a wash of sympathy. They all wanted answers but she could see he was struggling, punishing himself for not being able to take any immediate action. It was hard for him and he completely understood. "You could always go down and see Rodney," she suggested, "check how he's doing?

"I should stay here." The words felt heavy and he breathed out a sigh, his gaze drawing back to Elizabeth'she pale features. She looked so frail and vulnerable beneath the crisp white sheets, and he waved a hand between them, "besides... Rodney thinks I could be contagious remember?"

"That's not why he left." Even as she said it she knew the comment didn't hold a lot of weight. Rodney had been trying to help but there was no denying that her boyfriend been grateful for a reason to keep away from the infirmary. "Okay maybe it is-" she conceded, "but he had a point, he's more useful down there."

John merely shrugged in response and she got the feeling it wasn't just annoyance keeping him stationary. Despite everything the two men were friends and she sensed there was more leading to his hesitation. "You're worried he's going to ask about the two of you."

It was more or a statement than a question but it still made him uncomfortable. "It's not exactly something I want to talk about right now."

He tensed and she took a deep breath hoping she wasn't stretching their own friendship. She had a habit of sometimes pushing her opinion at inappropriate times -something she and Rodney had in common- but she owed it to Elizabeth to at least try. "It could help, might make you feel better?"

"It's McKay," he said flatly, folding his arms across his chest. If he wanted emotional support he'd be better off trying his luck with a Wraith queen.

She didn't say anything in return and an awkward silence followed drawing a sigh from his lips. He sometimes forgot that the two of them were a couple and he forced an apologetic smile in her direction, " _sorry_..."

She accepted the apology, patting his shoulder lightly, "just think about it, I know he could use the help... even if he won't admit it."

It was the understatement of the century but he bit his tongue glancing down at Elizabeth as the doctor left them alone. He felt useless and even though searching the database was like looking for a needle in a haystack, maybe Keller was right.

Maybe actually doing something would help ease the fear threatening to suffocate him.

xx

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AN: Another short one, I'm sorry! Only one more short one then I promise the next one will be longer 3 Also it's very late so please forgive any typos xx


	8. Chapter 8

"Need help?" John asked, shuffling into the dark lab. McKay was at work swiping information back and forth over a glass monitor and even though he felt out of place he stood his ground waiting for the scientist to acknowledge hum.

Rodney turned his head letting out an automatic response, "from you?

The tone was judgmental, built from his frustrations but he quickly came to his senses and softened his demeanor. Jut because he couldn't find the answers he was looking for, that didn't mean he should take it out on his team. Especially not the man in front of him. "Lorne and Elizabeth?" He asked, turning back to his work.

"Still no change." John confirmed, digging his hands in his pockets, "how's that plan b coming along?"

"It's not." He sat back down in his chair, pulling up the automatic search he'd been running, "there's no information in the Atlantean base that matches this virus. Maybe if we went back to the planet-"

" _You_ want to risk going back?" John raised his eyebrows skeptically, moving further into the small space. There was active equipment everywhere but it was useless unless it could help Lorne or Elizabeth.

"Well no, obviously not _me-"_ he confirmed tapping the keyboard, _"_ but a hazmat team. They could ask the locals some questions, see if they've encountered this strain before."

John nodded having already set the plan into motion. Even though there was a high level of risk associated with sending a team back he'd cleared it with Woolsey the second Evers and Green had been given a clean bill of health. "Already got the go-ahead, they're leaving in twenty minutes."

"You're not going?" Rodney stopped what he was doing, swiveling around in his chair and swallowing his next comment. The man looked exhausted, his expression barely readable in the dim light but it didn't come as a surprise. For once, he got it. If it was Jennifer he wouldn't want to leave her side either and the notion prompted an impulsive question. "So... you two are-"

" _McKay_ ," John cut him off with a warning tone.

"Not talking about it-" Rodney held up his hands in surrender, "message received loud and clear."

John breathed out, glancing around the room, "so where do I start?"

Rodney pointed to the desk behind him, handing over a piece of paper with Atlantean writing scrawled over the page. "Over there. If you see any of these words stop scrolling."

John nodded, not sure he would be of much help but grateful for the distraction. It would be at least an hour and a half before he needed to check in with the team gating offworld and for once McKay seemed to understand the need for silence. A good thing because his head had started pounding and he wasn't sure he could deal with any questions.

Not until he knew for sure Elizabeth was going to be okay.

xx

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 **An: Sorry, another short one but they will get longer :)**


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